## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
| patient | ID | age_at_sample_exact | cell_type | phase | BaitLabel | |
|---|---|---|---|---|---|---|
| 3 | PD4781 | PD4781f | 81.77139 | PB Gran | Recapture | PD4781f |
| 4 | PD4781 | PD4781g | 82.02053 | PB Gran | Recapture | PD4781g |
| 5 | PD4781 | PD4781h | 83.36208 | PB Gran | Recapture | PD4781h |
| 1 | PD4781 | COLONY84 | 83.81930 | BFU-E-Colony | Colony | NA |
| 6 | PD4781 | PD4781i | 85.58522 | PB Gran | Recapture | PD4781i |
| 2 | PD4781 | COLONY86 | 86.02327 | BFU-E-Colony | Colony | NA |
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)
Note that the different colours on the tree indicate the separately fitted mutation rate clades.
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## -0.0000 0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 15.2797 0.8644 17.6760 <.0001 13.5855 16.9740 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
| node | driver | status | child_count | type | colony_count | mean_lambda_rescaled | correction | sd_rescaled | lb_rescaled | ub_rescaled | median_rescaled | p_lt_wt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -1 | WT | 1 | -1 | local | 1 | 15.27972 | 1.0798 | 0.7472428 | 13.86324 | 16.79247 | 15.26507 | NA |
| 66 | TET2,JAK2,9pUPD,7p-,7q- | 1 | 56 | local | 56 | 23.96258 | 1.0798 | 2.7250445 | 19.04924 | 29.48395 | 23.87934 | 0.000050 |
| 120 | DNMT3A,PPM1D,JAK2 | 1 | 4 | local | 4 | 20.21356 | 1.0798 | 1.9553184 | 17.74161 | 25.14174 | 19.73444 | 0.000625 |
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
| patient | node | driver | child_count | lower_median | upper_median | lower_lb95 | lower_ub95 | upper_lb95 | upper_ub95 | N | group | age_at_diagnosis_pcy | max_age_at_sample | min_age_at_sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD4781 | 120 | DNMT3A,PPM1D,JAK2 | 4 | 0.025686 | 55.83527 | 0.0181318 | 0.0472691 | 52.18561 | 62.46789 | 6 | JAK2 | 74.18207 | 86.75154 | 82.49966 |
| PD4781 | 66 | TET2,JAK2,9pUPD,7p-,7q- | 56 | 0.025686 | 67.47880 | 0.0181318 | 0.0472691 | 62.94302 | 70.86795 | 6 | JAK2 | 74.18207 | 86.75154 | 82.49966 |
## Timings using the Clade Specific Rates
| label | node | het.sensitivity | chr | start | end | nhet | nhom | mean_loh_event | lower_loh_event | upper_loh_event | t_before_end | t_before_end_lower | t_before_end_upper | kb | count_in_bin | count_se | pmut | pmut_se | xmean | xse_mean | xsd | x2.5. | x50. | x97.5. | xn_eff | xRhat | lmean | lse_mean | patient | driver3 | child_count |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9pUPD | 66 | 0.9897 | 9 | 41634 | 20134580 | 1 | 5 | 54.89 | 35.94 | 65.62 | 12.42 | 1.689 | 31.37 | 20100000 | 3508 | 59.23 | 0.007661 | 0.0001294 | 0.8154 | 0.000725 | 0.1163 | 0.53373 | 0.8369 | 0.9749 | 25752 | 0.9999 | 7.927 | 0.000881 | PD4781 | TET2,JAK2,9pUPD,7p-,7q- | 56 |
| 9pUPD_B | 122 | 0.9398 | 9 | 41634 | 33877116 | 2 | 1 | NA | NA | NA | NA | NA | NA | 33800000 | 6732 | 82.05 | 0.014702 | 0.0001792 | 0.4746 | 0.001300 | 0.2054 | 0.09164 | 0.4749 | 0.8525 | 24965 | 0.9999 | 4.223 | 0.000318 | NA | NA | NA |
Here we exclude all local CNAs and depict as color VAF plots